Variant report

Variant	rs6083737
Chromosome Location	chr20:25058871-25058872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:25058740-25058890	HCM	heart:	n/a	n/a
2	TCF12	chr20:25057128-25058878	A549	lung:	n/a	chr20:25058651-25058661
3	E2F6	chr20:25058180-25058924	A549	lung:	n/a	chr20:25058551-25058561
4	MAX	chr20:25058125-25058971	A549	lung:	n/a	chr20:25058692-25058702 chr20:25058694-25058701 chr20:25058691-25058700 chr20:25058693-25058702
5	MAX	chr20:25058080-25058985	A549	lung:	n/a	chr20:25058692-25058702 chr20:25058694-25058701 chr20:25058691-25058700 chr20:25058693-25058702

No.	Distal block	Cell Line	Cell type
1	chr20:25058836..25060785-chr20:25065657..25068597,2	K562	blood:
2	chr20:25056370..25059250-chr20:25174569..25177571,3	MCF-7	breast:
3	chr20:25057289..25058975-chr20:25226619..25228863,2	MCF-7	breast:
4	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:

Variant related genes	Relation type
VSX1	TF binding region
ENSG00000197586	Chromatin interaction
ENSG00000100994	Chromatin interaction
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005409	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265721	0.80[EUR][1000 genomes]
rs7266451	1.00[ASN][1000 genomes]
rs7344824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25057200-25060600	Enhancers	Dnd41	blood
2	chr20:25057600-25059000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr20:25057800-25059000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:25058000-25059000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr20:25058000-25059000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:25058000-25059000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr20:25058000-25059000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr20:25058200-25059000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr20:25058200-25059000	Active TSS	A549	lung
10	chr20:25058400-25059000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
11	chr20:25058600-25059000	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr20:25058800-25059000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
13	chr20:25058800-25059000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr20:25058800-25059000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr20:25058800-25059000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr20:25058800-25059000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:25058800-25059000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr20:25058800-25059000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:25058800-25059000	Enhancers	Liver	Liver
20	chr20:25058800-25059000	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr20:25058800-25059000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr20:25058800-25059000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr20:25058800-25059000	Bivalent Enhancer	HSMMtube	muscle
24	chr20:25058800-25059000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
25	chr20:25058800-25059200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:25058800-25059200	Bivalent Enhancer	Fetal Heart	heart
27	chr20:25058800-25059200	Bivalent Enhancer	HepG2	liver
28	chr20:25058800-25059400	Weak transcription	Colonic Mucosa	Colon
29	chr20:25058800-25061800	Weak transcription	Pancreas	Pancrea

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